Tuesday, February 27, 2007

Now that the radical conservatives have been temporarily beaten back from the State Board of Education, they are trying a new tact to control schools. Lance Kinzer from Olathe has proposed a bill to strip primary and secondary school teachers from protections against laws related to obscenity.

Kansas has been at the center of a number of controversial book decisions that have upset conservatives and it seems that this bill is an attempt to muzzle teachers ability to select materials deemed offensive to delicate religious conservative sensibilities. It is not enough that school districts already have opt out provisions for parents who might object to certain material, now the conservatives lead by Kinzer want to control what all kids are exposed to regardless of what parents might want.

Monday, February 26, 2007

An alleged alternative to Wikipedia has been making the rounds of the noosphere. Personally I suspect it's an early April Fool's joke. Nobody in the 21st century believes stuff like this:

"Creationists believe, based on archeological and Biblical evidences, that dinosaurs were created on the 6th day of the Creation Week[1], between 6,000 and 10,000 years ago; that they lived in the Garden of Eden in harmony with other animals, eating only plants[2]; that pairs of various dinosaur baramins were taken onto Noah's Ark during the Great Flood and were preserved from drowning[3]; that fossilized dinosaur bones originated during the mass killing of the Flood[4]; and that some descendants of those dinosaurs taken aboard the Ark still roam the earth today[5]."

Sunday, February 25, 2007

OK, grab a warm spot and a cat! Lets see what's up among Kansas bloggers this past week.

First up Bruce Alderman over at It Seems to Me discusses the Kansas State Legislature's failure to pass a minimum age law. He notes that some of sharpest disagreement that a minimum wage is needed comes from one of the richest counties in the state and argues that "If we can't find a way to ensure a living wage for full time work, then we don't deserve to survive long as a society."

Mike Silverman continues the political theme with an analysis of the highly charged Lawrence City Commission race.

Another political development is the primary for Johnson County Community College's Board of Trustees and Mousie Cat over at Evolving in Kansas has made her endorsements. This race is extremely important since according to some counts the college is the third largest educational institution as a state. Mousie and I agree on our endorsements by the way.

Pat Hayes over at Red State Rabble notes that the recent ruling in Massachusetts that parental rights were not violated when schools exposed their children to ideas contrary to religious beliefs, might have implications here for the evolution battle.

Speaking of religion, Bill Tammeus(not a KGB member) in his Faith Matters Blog observes that couples spend more time on planning the wedding than on marriage preparation.

"This charismatic movement that wants to take the standards of holiness and separation out of the Church and replace it with a ‘cool’ and ‘trendy’ church is the work of hell. The devil knows what God is looking for in His bride and it ain’t what we are seeing all over our country in these worldly churches."

There has been a row over a chicken tossed onto the basketball court during KU's win over KSU according to Emawkc at Three O'Clock in the morning. He also reveals an adolescent hobby. Personally when I think Jayhawk, I think terror bird.

Jon Voisey, the normally Angry Astronomer celebrates his 300th post with a set of KU pictures-OK some are of the night sky but that's OK. But Jon can you prove those points of lights are really stars?

John B. who co-hosts KGB has been making really annoying scraping sounds against the bottom of the well of inspiration and manages to pull together some pithy commentary on some his favorite bloggers. Josh our other co-host is upset at goings on at the Smithsonian Institution.

Gwynne at the Shallow End has had a busy week amongst which she reports on the Dead Sea Scroll exhibit at Union Station. Unfortunately, she was underwhelmed by the exhibit. Joel Mathas had mini cultural event of his own, meeting someone who was a major childhood inspiration-would that we would all be so lucky!

Just in case you don't have a cat-I leave you with a short poem and commentary titled A Mammal in Winter.

Friday night we went to see Delirium, Cirque du Soleil's arena touring group, at Kemper arena in Kansas City. Delirium is Cirque du Soliel's attempt to bring some sort of tribal experience to a large arena and it is quite different from the more acrobatic Cirque du Soliel shows that the average person is familiar with. Rather than performing in the round, the audience is on one side of a large central stage flanked by two huge projection screens. The central stage is at various times curtained off by a very thin material that also can have images projected on it. The images, the music and the performers are very tightly integrated.

The choreography is stunning and Delirium shows what can be done with light to give texture. During part of the show a series of tribal dancers were hunched on a large moving mushroom complete with drums and as the lighting shifted the dancers became more like black and white poison arrow frogs clinging to the mushroom. I don't know if that specifically was the intent, but the effect was quite striking. At other times the effect was like peering into a large surreal water filled aquarium with human fish floating around, layers upon layers of texture built up entirely with lights.

We enjoyed Delirium but I don't think the audience as a whole got quite what they expected. A number of people left before the end and most of the rest of the people were somewhat reserved in their reactions. Part of the problem may simply have been the venue. We were way up in the third tier of seats-you know the seats where oxygen masks are required if the air pressure gets too low. We could see and hear the show fine-the problem is that the arena audience is so spread out that the audience members never were able to connect with each other in the sort of tribal way that it seems Delirium is trying to foster.

Probably those on the main floor got a better connection with each other and with the performers since performers did interact directly with them and it seemed that the producers are really trying to overcome the limitations of the sterile arena setting. They just can't quite pull it off yet- at least not for a tough Kansas audience. Maybe the producers can find some little trick or thing for those in the auditorium as a whole to do especially toward the end and their wonderful climax, even if only some of those big balloons that were bounced around on the arena floor made it to where we were.

Kansans get another chance to see Delirium at the Kansas Coliseum in Wichita March 12 through the 14th at 8:00 pm. If you go in expecting to see lots of exciting acrobatics you may be disappointed, but the show is stunning. By the way, the pictures on the Delirium web site do not do justice to the special effects. Also we took binoculars and while they were nice to have to see details of some of the costuming, they really were not needed as much of the action on the main stage is integrated into the imagery projected on the side panels.

Saturday, February 24, 2007

With a furnace of her ownShe stalks into the night.Her eyes, her lipsAre stars to whichI am drawn.Her heat warms myWintered heart.

Sometimes one finds a line that just begs to be used in a poem-the line here being the title of a wonderful article in a recent NY Times Science (Feb 20)section by Natalie Angier. The article is about the advantages and disadvantages of being warm blooded, something I often use as a case study about adaptations. In fact I just talked about this article as part of a discourse on thermodynamics to my introductory biology class.

The article's title is a real grabber and I just had to do something with it, hence this poem for my wife. The CAT though thinks it's for her.

That's right! Its time to submit your best Kansas blogging for the Kansas Guild of Bloggers "Hot cat on a cold night edition". So point me to your best blogging and pictures and poems, be you a Kansas blogger blogging about what ever, or a blogger where ever blogging about Kansas. We may not be posted until late Tuesday so you have a bit of slack. You can either submit your entries to the KGB carnival page or e-mail them to me directly at pdecell@sunflower.com. Oh and be sure to check out this week's KGB at Thoughts from Kansas.

Wednesday, February 21, 2007

So much depends on a levee made of sandHolding the sinking land from the river,The water eating away at its baseAs houses are built by the blindAnd the deaf and the mute,Houses like capsids amidst the lawnsPlated on petri dish earth.

So much depends on consequence delayedAnd creaking pumps sucking what would beAs fast as it comes in like a blind snakeHunting a mouse.So much depends on those constructed thingsBig and leaky on the edge of disaster.

And yet, surrounding each cell the mosaic assembles itself blindlyAs lipids jostle each other and proteinsShape themselves into pumps and channels,A levee of sorts way beyond paper thin,but that keeps at bayWhat otherwise would be.

This week's Poetry Thursday prompt is 'The Body Knows' and that is reflected in this poem which contrasts our ability, or lack there of sometimes, to avert disaster and depend on our technology even though we use it in a shorted sighted almost blind way. And yet we depend on processes that are also blind in terms of the intricate operation of each of our cells. There is nothing mystical here. After all, the pumps and channels I refer to after all arise through the evolutionary process- the intricate blindness of the title.

So I am contrasting two types of blindness. The first type comes about because of our own political and analytical shortcomings which unless we recognize and account for them lead to disaster. The second type of blindness is that of the evolutionary process which has had 3.5 billion plus years to do what Daniel Dennett refers to as R and D or research and development leading to the marvelous adaptations exhibited by the body. This intricate blindness gives rise to the illusion that 'the body knows.'

The poem's first lines about levees are inspired by a discussion on NPR this morning about how ill prepared we are to deal with disasters, the example used being the fragility of the levee systems in the Sacramento California area. The discussion was with the author of a new book called The Edge of Disaster. See this link for another review.

The poem is also inspired by another interesting review of a book, this time on the limitations of mathematical models of natural phenomena:

Monday, February 19, 2007

Problems can be avoided if you take HAVIDOL only when you are able to immediately benefit from its effects. To fully benefit from HAVIDOL patients are encouraged to engage in activities requiring exceptional mental, motor, and consumptive coordination. HAVIDOL is not for you if you have abruptly stopped using alcohol or sedatives. Havidol should be taken indefinitely. Side effects may include mood changes, muscle strain, extraordinary thinking, dermal gloss, impulsivity induced consumption, excessive salivation, hair growth, markedly delayed sexual climax, inter-species communication, taste perversion, terminal smile, and oral inflammation. Very rarely users may experience a need to change physicians. Talk to your doctor about HAVIDOL.

I expect a gene, probably on chromosome 2, is linked to this disorder.Technorati tags:humor,

Phelps is well known for his militant antihomosexuality. The sad thing is that it took Phelp's looney bin attempts to link gays to 9/11 and his picketing of military funerals to get people really upset at him.

Of course is Phelps really any worse than Carl Burkhead who hides his dislike of homosexuals and opposition to anti discrimination laws because he thinks he understands God's law and claims to hate the sin and not the person? Somehow the notion that employment is essential to the dignity of the person escapes Burkhead and to be fair many in my own Church who claim to be for human dignity.

At least Phelps is honest as is Tim Hardaway who allegedly said in a radio interview:

"You know, I hate gay people, so I let it be known. I don't like gay people and I don't like to be around gay people," he said. "I'm homophobic. I don't like it. It shouldn't be in the world or in the United States."

What I love is the 'new' antihomosexual position that blames gays for any discrimination they encounter. This came out the other day in the hearings related to a proposed state wide antidiscrimination law now stalled in committee. An opponent of this bill, Republican Janet Paul allegedly said in committee:

“Those of a different sexual orientation are not visible in our society unless they choose to be...”

Monday, February 12, 2007

What we are celebrating is not so much Darwin as a person or scientist but really a new way of seeing the universe the fruits and implications of which are still being digested by some people in our society. Darwin took the scientific viewpoint and extended it to the issue of design through three radical ideas:

1. Variation is important for how evolution operates rather than being accidental.2. Biological evolution -Descent with modification- is a population phenomenon.3. The complex adaptations that organisms show arise by natural processes which can be understood.

This week I will be starting a series of posts exploring Burt and Trivers new book Genes in Conflict which really is about the implications of Darwin's ideas to molecular genetics. My first post on this book is here so I recommend reading it first to get a flavor for what Burt and Trivers are trying to do.

Sunday, February 11, 2007

We often think of invasive or noxious species as exotic species that have come to a new area from some far off place-examples include the starling, fire ants, zebra and quabba mussels, or kudzu. Indeed here in Eastern Kansas its difficult to find a habitat that doesn't have it's complement of these sorts of invasive species. Yet some native species have characteristics of invasive species. A good example in Kansas is the red cedar.

Red cedar is not a true cedar but is a juniper (Juniperis virginiana). I've always had mixed feelings about this tree. On the one hand it is great for many species of wild birds since it both provides shelter and food in the form of these berries from a USDA website:

When relatively scarce it can provide a nice contrast in the land scape. On the other hand it is very invasive. For instance I don't have any red cedars in my yard but have to constantly fight the seedlings in my garden. It seems they just happen to germinate in those areas of the garden where I have my prized butterfly weed growing-an invasive species battle on the small scale. Red Cedar's native range is throughout much of the Eastern United States and west through Central Kansas. Indeed, the Red cedar is Kansas' only native conifer. A good range map is here from the United States Geological Survey's website.

So if it is a native species-why is it classed as an invasive species? First of all it is an exotic invasive species in certain parts of the United States, in both Oregon and Hawaii. Next within its and around its native range, the Red Cedar is spreading into grassland systems where it allegedly reduces the productivity of range land by altering the microclimate around the trees which encourages the growth of less desirable non native cool season grasses, according to the Nebraska Extension Service.

The Nebraska Extension Service has some interesting tidbits on control. Complete eradication is not feasible and probably not desirable. Fire seems to be the most effective control where feasible especially when the trees are small. The extension service also says that goats have been used as control, and recommends 10 goats per acre in lands that can be fenced and expect to let the goats graze for several years or else the trees will recover.

This image shows my own little cedar problem. These seedlings appear to have germinated from mulch I obtained from the City of Lawrence's mulch program or from a local garden store.

So what we have in red cedar is a species, that has at least some of the characteristics of more traditional invasive species: adaptability to many habitats, suitability as an early successional species, rapid dispersal, ability to crowd out other species by direct competition for resources by altering microclimate and indirectly by allelopathy. Further the spread of this species into new habitats appears to be related to human interference with these habitats. In the case of red cedar and the prairie ecosystems its spread appears to be facilitated by suppression of the fires that maintain the open prairie combined with loss of large grazing herbivores especially the bison, an issue discussed by Collins et al(1998).

Whether red cedar is called an invasive species or just a noxious species really hides the more important issue, that the ecosystems of this planet are being altered by human activity at an increasingly rapid rate, bringing about unpredictable changes in the ecosystems of this planet. This is true even in the absence of the current focus on global warming. Like it or not we are creating a global flora and fauna, consisting of those relatively few species who just happen to have a mix of characteristics that enables them to survive the effect of human disturbance.

My own belief is that we are long passed the point where most of the planet's ecosystems, at least terrestrial and freshwater aquatic systems, are robust enough to survive the rapid changes we as a species are making without management. We can talk about creating reserves to preserve some remnant of biodiversity as E.O. Wilson has, but unless we have a global consensus that we need to manage the affects of human disturbance, the long term prospects for maintaining some significant fragment of biodiversity at all levels of scale are not good.

By the way if you are interested in keeping up with the latest on invasive species, Dr. Jennifer Orth has a wonderful blog called appropriately the Endangered Species Weblog. (oops update! Poor Jennifer...as Dave points out it's Invasive Species Weblog....)

Friday, February 09, 2007

Since my last few posts have been mainly text and since it is Friday afternoon I thought I would have some fun. Second Life (SL) is a 3 dimensional virtual world which people can join and do pretty much anything. It has its own economy and currency, has its own scripting language which you can use along with building tools. Second Life has begun attracting educators with the potential of providing an immersive and interactive experience for students.

So in the spirit of the Just Science Challenge I decided to see what SL has to offer in the way of Science. I started out at Second Life's Science Center at Info Island II (115, 204, 24). The Center has a few exhibits; my favorite being this large caffeine molecule.

SL has a physics engine which you can turn on or off for objects you create and here is a demonstration of a gravity well which exploits the physics engine to show how objects behave in a gravity well.

But the Science Center serves as a portal to other second life science sites and the one that caught my eye is the International Space Museum (ISM) and this turned out to be quite a treat and shows the potential of SL for an immersive experience.

When you teleport to the ISM, this wonderful display greets you.

"Earth is the cradle of humanity but one cannot live in a cradle forever."

The site has a huge collection of very realistic rockets and other space craft from all over the world.

The big brown rocket with the black upper stage is a Japanese Space Agency Rocket used to launch multiple satellites.

A over all view of the Space craft exhibit showing me in black chatting with another visitor.

Who else is old enough to have seen this capsule?

You can't enter this mock up but in another part of the museum is a box that you enter and find yourself inside this capsule. My picture does not do justice to being inside the capsule! This is a mock up of the inside that uses actual photos of the inside very cleverly. No, this is not the Space Shuttle.

Next is a Saturn V and its umbilical tower. Looking up from the base:

Unmanned space exploration is not ignored either as these shots show; the craft on the right is Voyager which has long left the solar system.

There is even a robotic arm you can play with. Looks like the one from the Shuttle:

And of course the latest ummm thrust toward the privatization of space is represented by this spiffy Spaceship I. This mock up actually flares and sounds like the sound of the actual engine firing was used for the audio.

Well eventually I had to teleport to my home and do some real work so here I am in my Second Life homestead...called, what else, but Mendel's Garden. By the way if you haven't visited this month's Mendel's Garden at Genetics and Health, please do so to get the best of recent genetics blogging. Also if you join Second Life, tell them Simeon Gateaux or Simone Gateaux sent you...I do get a small referral bonus in the SL currency.

Second Life links mentioned in this post: These are SLurls and clicking on them will take you to a map showing the location of the site in the SL world. If you have SL installed you can teleport to the site.

Thursday, February 08, 2007

One of the books I am reading right now is Austin Burt and Robert Triver's(2006) Genes in Conflict from Harvard University Press. An outline of the chapters is here. The basic premise of the book is that genes in an organism don't always agree and may spread even though the individuals bearing the genes may have reduced reproductive success. So these genes are a type of selfish genetic element which Burt and Trivers more precisely define as

"...stretches of DNA (genes, fragments of genes, noncoding DNA, portions of chromosomes, whole chromosomes, or sets of chromosomes) that act narrowly to advance their own interests-in other words, replication at the expense of the larger organism." p 2.

This notion is not entirely new. After all, early on in the 20th century geneticists discovered meiotic drive where genes or chromosomes can spread by distorting the 1:1 segregation ratios expected during meiosis. So for instance if you have an individual who is heterozygous Aa, we expect that half the gametes will have the A allele and half the a allele. But in meiotic drive this segregation ration is distorted and this bias can cause the spread of the allele biased for by meiotic drive even if the over all Darwinian fitness of the individual is reduced.

In what may seem contradictory, Burt and Triver's work is an extension of W.D. Hamilton's work on kin selection in which a a gene that reduces an individual's reproductive success (classical Darwinian fitness) may spread if the individual bearing the gene, increases the reproductive success of kin. This can work of course since kin are more likely to have copies of the gene. Much of Triver's work early on was in the area of genetic conflict vs cooperation among interacting organisms say parent offspring or even between interacting species as in the notion of reciprocal altruism.

I like Burt and Triver's book because you don't have to read it straight through and I often dip into it for good examples of how genes act...and these are relatively independent of whether or not you have read the rest of the book. The other nice thing about the book is that it integrates population thinking with molecular genetics in a very natural way, so that molecularly oriented biologists will hopefully begin to think about how these systems arise and behave in an evolutionary framework. On the other hand more classically trained population genetics types will begin to think less simply about the mechanisms involved in the systems we try to model at the population level. Also Burt and Trivers are careful to point out when information is lacking either at the molecular or at the evolutionary level.

Without going through the whole book here are a couple variations on the selfish genetic elements covered by Burt and Trivers. First are selfish sex chromosomes. For instance while in mammals males are usually XY and females XX, in some rodents there are 'feminizing' X and 'feminizing' Y chromosomes (denoted X* and Y*) In those rodent species with feminizing X* chromosomes along with regular X chromosomes there are three types of females possible XX , X*X, and X*Y and only one type of male XY. Notice that when the X*Y female mates you end up with the following situation:

1/4 of the zygotes will be X*X (female), 1/4 will be X*Y (female), 1/4 XY(male) and 1/4 YY. The YY individuals are not viable so that means the X*Y females have reduced individual fitness. Yet even in the simplest situation the X* chromosome can spread until it becomes so common that individuals with the X chromosome out produce them.

Another variation of on the theme of selfish genetic elements is genetic imprinting. In genetic imprinting the expression of a gene is dependent on which parent the gene is from. Classically for instance the phenotype of a heterozygote (Aa) is not affected by which parent donates the two alleles. In mice a gene called Igf2 is only expressed if inherited from the father. If this gene is inherited from the mother it is not expressed or maternally imprinted. There is no change in the nucleotide sequence in these imprinted genes, but the some of the nucleotide bases are methylated in the imprinted genes. One interesting thing about imprinting is that the the imprinted status of a gene is reversed from one generation to the next in the germline. First, the DNA methylation is removed and then the sex appropriate imprinting is done. So for instance for Igf2, the imprinted copy of this gene inherited by a female mouse from the father will not be expressed. But in her germ cells, the methylation is undone and that unimprinted gene is passed on to her offspring! Conversely for a male mouse the unimprinted copy of the gene from his mother is methylated in his germline cells.

Clearly this sort of regular system must have an evolutionary origin and Burt and Trivers nicely review the hypotheses about the origin of this system. Their thesis and the thrust of other researchers in this area is that imprinting arises because of a conflict between genes of maternal origin versus those of paternal origin. This conflict may be played out in the way different genes affect investment in the fetus and fetal growth rates. To see why consider a mother who mates with only one male in her life. There should be no conflict between these parents over how much parental investment to make in the offspring, since both parents loose equally say if the offspring uses to many resources during development.

But suppose the female mates with more than one male in her life or all the offspring are sired by different males. Then those males who pass on genes that increase the growth rate of their fetus at the expense of those of other males would have the advantage, even if this rapid fetal growth rate harms the mother to some degree. The mother on the other hand would benefit most by suppressing (imprinting) those genes that are paternally active and activating genes that benefit her interests. Probably the best way to say this is that the parents have a conflict over which sets of genes tied to development best serves each parent's interest.

Burt and Trivers view it as no accident that most of the 100 or so genes (out or 30,000 in the human genome) that are imprinted are fetal growth related. For instance the Igf2 gene is paternally active(maternally imprinted) and it increases size at birth by about 40%. The Igf2r gene in mice is maternally active(paternally imprinted) and it has the affect of decreasing size at birth. So these genes are acting in opposite ways and tend to cancel each other out in terms of net effects, exactly according to Burt and Trivers, what would be expected to be the evolutionary result of a conflict between maternal and paternal interests.

If your head is spinning, welcome to the club. Probably the best statement of what Burt and Trivers are getting at here is in the very last paragraph in the book:

"The unity of the organism is an approximation, undermined by these continuously emerging selfish elements with their alternative, narrowly self-benefiting means for boosting transmission to the next generation. The result: a parallel universe of (often intense) sociogenetic interactions within the individual organism-a world that evolves according to its own rules, as modulated by the sexual and social loves of the hosts and the Mendelian system that acts in part to suppress them."

So yes, cooperation is important in evolution but even within the individual organism genes don't act in a united fashion, for rogue genetic elements favoring one interest over another are constantly arising and at a very basic level the individual organism and it's genetics are shaped by this fact.

Tuesday, February 06, 2007

When I took evolutionary theory as an undergraduate one of the concepts we learned about was that of of a hopeful monster-a radically new form of an organism arising, say by mutation. The hopeful part refers to the idea that these abruptly produced form might be adaptive in it's environment. The prevailing thought today is that this sort of leap probably doesn't happen at least not in the way envisioned by it's proponents.

A recent paper by Joanna Masel in Genetics 172:1985-1991(2006) takes a fresh look at the hopeful monster issue in terms of a model of two types of mutations that she calls "Hopeful monster" mutations and conversely "hopeless monster" mutations. Her use of these terms is crucially different than other uses because they refer to the fitnesses of the mutations rather than to a large phenotypic change. A "hopeful monster" mutation has reduced fitness in most environments but only slightly reduced fitness and may be adaptive in certain rare circumstances if the environment changes. "Hopeless monster" mutations have greatly reduced fitness in all environments.

Most of the time, both types of mutations ought to decrease in frequency relative to the alleles with the highest fitness in a particular environment. But what about when the population is subject to reduced selection for a time? Various authors cited by Masel have speculated that this sort of reduced selection, or as she terms it "shielding" may lead to a build up of potentially adaptive combinations of mutations when the environment changes and the mutations then become subject to natural selection. But she notes that this idea is controversial; After all if a population is adapted to it's environment then it is unlikely that a mutation will arise that will make it more adaptive.

From the point of view of her model, both sorts of mutations may accumulate when selection is muted or "shielded" but possibly adaptive combinations of "hopeful monster" mutations might be swamped by the fitness effects of hopeless monster mutations.

Masel investigates a simple model of a haploid population and she makes a number of simplifications to make the mathematics tractable, a very common strategy in population genetics. Indeed rather than being just two classes of mutations based on fitness effects it is more likely that there is a broader range of fitness distributions. She also assumes that the shielding or 'hiding' parameter S2 is constant across all mutants. So for instance in terms of selective coefficients, the fitness of a "hopeful monster" allele would be 1-S1*S2 where S1 is a small selection coefficient. For a hopeless monster allele a corresponding fitness would be 1-S2 since she makes the simplifying assumption that when these alleles are lethal. This may seem confusing but if the hopeless monster mutant is lethal then its corresponding selective coefficient when S2 is one is itself 1.0.

Another assumption she makes and one I wonder about is an assumption that environmental change is rare relative to the time scale of genetic drift, something that may not be true for very large populations. However this seems a conservative assumption since large populations are exactly the sort of populations where her model ought to work best, if it is going to work at all.

Her simplified model yields some interesting results. First of all her results suggest a Goldilocks effect with respect to when selection is weakened (S2 <>> 1/U. Again this makes some sort of sense, if most mutations that arise are of the hopeless monster sort, then it should difficult for potentially adaptive mutations to be maintained as part of the variation when selection is weakened.

What is really interesting is that the amount of potentially adaptive cryptic genetic variation that accumulates when selection is shielded is increased as deleterious mutations accumulate when selection is weak. This affect is enhanced, according to her model, for adaptations that might require particular combinations of mutations. She claims this is relevant to theoretical attempts to estimate the rate at which adaptive combinations of mutants might arise, which she sees as significantly underestimating this rate because the do not account for the enrichment of "cryptic" genetic variation when selection is relaxed.

She then discusses some situations where her model's concepts might apply. For instance yeasts have a prion called PSI+ that when it appears, clumps the non prion protein Sup35, depleting this protein. Sup35 is a termination factor for translation so the effect of removing this protein is to cause the ribosome to increase the rate at which it reads through the normal termination site, exposing cryptic variation presumably in the normally untranslated trailer region of the RNA.

It seems to me that good experimental systems might involve domestication especially in animals where domestication often seems to lead to relaxed selection on certain aspects of the phenotype. Presumably the affects of relaxed selection could be investigated in yeast or bacterial systems to mimic the effects of domestication. Her model is also relevant to the concept of preadaptation to which the term exaptation is applied today. She notes that the sort of cryptic variation she discusses can be "coopted" in the same way that a trait adapted for one function is often adapted for another function. Indeed she seems to be arguing for a use of the word preadaptation for populations in which the sort of enrichment of cryptic variation she postulates has taken place.

She also sees her work as relevant to an important theoretical question namely whether or evolvability itself can evolve. In other words perhaps mechanisms that allow populations to tap into hidden variation or otherwise evolve more rapidly might themselves might evolve. Personally I have been skeptical of this sort of thing, but maybe it is worth another look.

Monday, February 05, 2007

Now I am not a physicist or chemist but this article, "Nitrogen for Tires just hot air?" by Dave Toplikar in Sunday's Lawrence Journal World caught my attention. Apparently tire places are hawking nitrogen for tires rather than regular compressed air. One of Lawrence's tire places has recently installed equipment for filling tires with nitrogen at $5.00 a pop claiming that nitrogen filled tires hold their pressure three times longer than when filled with regular air. Tires filled with nitrogen also supposedly run cooler in the summer and since nitrogen is relatively inert, less corrosive to the innards of a tire than regular air.

Toplikar was rightfully skeptical of these claims because, recalling one of those facts that one should have learned if one was paying attention in school, or else watched the Discovery Channel, namely that "air" is about 78% nitrogen gas 21% oxygen gas with the balance being argon, water vapor, carbon dioxide methane and various other gasses. Since of the advantage of nitrogen supposedly rests with it being a bigger molecule, Toplikar asked the chair of KU's chemistry department about this and the chair gave an apt description of the relative sizes of a nitrogen molecule namely the difference is like a Chipotle burrito with lettuce vs one without lettuce.If there is any advantage to using pure nitrogen then is ought to rest with the reduction in corrosiveness but the chair was skeptical of that.

Molecular size is a bit tricky. As a quick comparison, we can use the covalent radius defined as 1/2 the distance between to identical covalently bonding nuclei. This is measured in picometers (1 pm= 1x 10-12 m). Nitrogen's covalent radius is 73pm so the length of a nitrogen molecule ought to be 4 X 75pm or 300 pm. A molecule of oxygen ought to be just a shade smaller 4 X 73pm or 292pm. So an oxygen molecule ought to be a little less than 3% smaller than a nitrogen molecule.

The companies that process nitrogen and make equipment for doing this tire filling are all for using nitrogen and there is even a Get Nitrogen Institute to promote nitrogen use including in tires. This site has a little link to "Deep Science" so let's see what is there. First is a "gas permeability table" (http://www.getnitrogen.org/pdf/GasPermTable.pdf). Now this gets the geek juices flowing. But the table makes absolutely no sense. It is basically a ranking of permeabilities with no units and no explanation of how the data were collected. Nitrogen gas and methane are both shown as having equally slow permeabilities and water vapor the worse, but beyond that there is no way to assess what these rankings mean. How much more rapid is the permeability of water vapor than nitrogen gas?

This "table" is typical of how promotional literature often times uses misleading graphics. Here is another promotion (http://www.matickchevy.com/Nitrogen.aspx) showing a huge apparent size difference between oxygen and nitrogen atoms when the real difference is a lot smaller.

Fortunately the site does provide some quantitative looking reports, for instance part of a thesis (http://www.getnitrogen.org/pdf/ubologna.pdf) on the use of nitrogen in tires suggesting from theoretical considerations that the permeability differences between nitrogen gas and oxygen that tires inflated with nitrogen gas should lose pressure at half the speed that tires filled with regular air.

So it's back to the web to look for articles relating molecular size to permeability through various sorts of films and found some interesting tidbits. For example at Stanford, scientists are attempting to use membrane separation to extract carbon dioxide based solely on molecular diameter which is the main determinant of diffusion if the pores in the membrane are at the nano scale, in line with the molecular sizes. (http://gcep.stanford.edu/research/factsheets/membrane_subnanoscale.html).

The idea is to use these membranes as a sieve to sort out the carbon dioxide produced by fossil fuels and the sequester it. There is a nice picture illustrating the concept. This suggests the tire rubber must have a complex of pores in the molecular size range of oxygen or smaller. Further it's likely that the nanoscale structure of these pores is makes the effect more like a series of sieves analogous to the sort of cascade of gas centrifuges used to sort out different isotopes of uranium by small differences in mass. So it is possible that small differences in molecular size lead to differences in permeabilities of a tire.

Getting back to tires, there apparently is benefit for freight truck tire longevity as described in this article (http://www.trucktestdigest.com/FeatureNitrogeninTires.htm). This article notes that a truck tire properly inflated might loose 2 pounds per square inch in three months as opposed to 2 pounds per square inch per month. But these are big semi tires. For space shuttle and other sorts of high performance tires maybe using nitrogen gas makes sense. These tires operate at much greater extreme of temperature and pressure than passenger car tires.

The car talk guys...and that's where I get my limited knowledge about cars have this to say about racing tires and nitrogen:

"One (i.e., Indy 500) racers use nitrogen in their tires because when you're traveling around an oval track at 200 mph, you want your tire pressure to be entirely predictable. They even "stagger" the tire pressure on those cars, making the outside tires a little fuller than the inside tires to keep the car turning inward. And at those speeds, an eighth of an inch in tire height can make a huge difference."

I suspect the predictability the car guys are referring to arises from the fact that regular air has water vapor in it so when the wheels cool, some of that vapor changes phase making the change in tire volume less regular.

Some of the advantage of nitrogen is also allegedly due to the fact that it is relatively inert compared to oxygen and one exhibit (http://www.getnitrogen.org/pdf/FordBaldwinResearchRaper.pdf) at the Get Nitrogen's "deep science" link attempts to address this. The study authors found that using nitrogen gas does indeed reduce the aging of tires and this seemed most pronounced for peel strength, the force required to separate the belts in the radial tires tested. But these tires were not run on passenger cars but 'cooked' for up to 12 weeks at 60 degrees centigrade. Indeed the study's authors note:

"Nonetheless, it is perhaps a fair assumption to say that there would be some improvement in tire durability if nitrogen was used as the inflation media, but it is too soon to speculate as to how much of an improvement it would be."

But does using nitrogen vs air in car tires make any difference for us as consumers? Probably not at $5.00 per tire when just periodic checking of pressure is sufficient, assuming of course we happen to have two quarters on us when we think about it to pay for the air. But this whole controversy illustrates how organizations can exploit a partial truth and through a little sleigh of hand can produce a new perceived need for the consumer.

By the way, in my searches I encountered a fascinating 19th century scientist who is not well known to non chemists, namely Josef Loschmidt who was the first scientist to estimate the size of molecules using the kinetic theory of gasses. There is a wonderful scientific biography for Loschmidt in Physics Today March 2001 which is online at http://www.physicstoday.org/pt/vol-54/iss-3/p45.html.

Sunday, February 04, 2007

We've had a pretty good run of cold weather this last week so it's time to curl up with your heater cat and check up on the state of Kansas Blogging.

Politics of course is a big preoccupation of Kansas Bloggers and we have yet another controversy, this time over a move by the Lawrence City Commission to set up a domestic partnership registry. Fellow Lawrence blogger Mike Silverman reports in his blog Red Letter Day, on an attempt by a conservative legislator to prohibit local governments from setting up such registries. Silverman claims that some conservatives favor local control until localities do something they don't like. Mike by the way is an avid Mac fan as you can see here.

Why is it that sex is such a threat to Kansans?Yours truly has had a snoot full with the people who are criticizing a proposal to require HPV vaccines for preteens. As you will see I am slowly loosing patience with various sorts of parental rights arguments when it comes to public health and child welfare and wonder if parents have the ethical and moral right to act against the child's best interest merely because of the parents religious beliefs.

"Sometimes, though, I get sick of myself. That’s where I was at the end of December. I was out of writing ideas, and I had enough other things to attend to in life that spending intellectual energy to say not much about not much seemed beyond narcissistic — it seemed an abuse of the privilege that is this forum."

Well I am glad he's back.

What would Kansas be without dialogue concerning creationism and Jon Voisey has been having a somewhat friendly dialog with another Kansas Blogger FTK(For the Kids) about stellar evolution. Check Jon's latest entry in the dialog here and FTK's (at Reasonable Kansans)here. They have managed to disagree and keep things civil so kudos for the two of them.